AbstractFive new species within the Australian carnivorous marsupial genus Antechinus have recently been named, at least two of which are threatened. Important facets of the habitat use and extinction risk of one of these new species, the buff‐footed antechinus, A. mysticus, are not well understood. Previous research has suggested that the species utilizes a broad range of inter‐connected forest habitats in southeast Queensland (Qld), Australia. Based on this potentially connected habitat, we predicted that A. mysticus should have low population genetic structure, particularly in relation to its congener, the spatially restricted, high altitude, closed‐forest A. subtropicus. We genotyped nine microsatellite loci for six populations of A. mysticus, sampled throughout their known range in eastern Australia, and compared them with four proximate populations of A. subtropicus. Surprisingly, genetic structuring among southeast Qld populations of A. mysticus was moderate to high and similar to that between A. subtropicus populations. We postulate that all A. mysticus populations have declined recently (<100 generations), particularly the northernmost southeast Qld population, which may be at risk of extinction. Our results suggest that A. mysticus is limited to a more scattered and fragmented distribution than previously thought and may be in decline. The identification of population decline in this study and recently in other Antechinus suggests the extinction risk of many Australian mammals should be reassessed.